Rigging an anatomical muscle
I think I have solved the problem of the hook modifier behavior by making custom vertex group hooks. I copied the vert group and assigned it but also made an exact copy as a separate mini-mesh. 
The shiny torus was manipulated with the hook technique I came up with today. If anyone else has trouble with hook behavior, perhaps I should upload the screen shots.
FYI the custom vert/hook objects are invisible on the torus but I parented them to the cylinders. I will try on real bones later.